Results for the regional assessment (PhD Chapter 1)


This series of files compile all analyses done during Chapter 1 for the regional assessment (Campaign 2016).

All analyses have been done with PRIMER-e 6 and R 3.6.0.

Caracteristics of each campaign

2014 2016 2017
Sampling date August-September June to August July
Criteria for perturbation Potentially impacted if close to the city or industries, References outside the bay Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria
Regions considered BSI BSI, CPC, BDA, MR BSI, MR
Number of sampled stations 40 (20 HI, 20 R) 78 (26 BSI, 19 CPC, 18 BDA, 15 MR) 126 (111 BSI, 15 MR)
Parameters sampled Organic matter yes yes yes
Photosynthetic pigments no yes yes
Sediment grain-size yes yes yes
Heavy-metals yes yes (for a limited number of stations) no (interpolated based on 2014 and 2016 values)
Benthic communities Compartment targeted Macro-infauna Macro-infauna Macro-infauna
Sieved used 500 µm 1 mm 500 µm and 1 mm
Conservation technique Formaldehyle Formaldehyle Formaldehyle
Others N.A. N.A. N.A.

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We selected variables and characteristic species (using IndVal index and SIMPER procedure, see Section 2) for the analyses:

As there is missing data for metal concentrations outside BSI, two Designs have been used:


Workspace preparation

Here, we use data from subtidal ecosystems (see metadata files for more information)
Only stations that have been sampled both for abiotic parameters and benthic species were included.
The script below includes personnal functions, refined data, parameters for each campaign and global means, sd, se.


Maps

1. General map

2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity.

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Cgra

Marc

Epar

Species richness

Total abundance

Shannon index

Piélou’s evenness

Analyses

1. Barplots

Depth

Organic matter

Grain-size

Heavy metals

This section is not relevant here, as we only have data for BSI.

Species abundances

Diversity indices

2. Phylum frequencies

Phylum abundances by region
Phylum BSI CPC BDA MR
Annelida 214 69 188 43
Mollusca 191 45 89 100
Arthropoda 119 13 30 43
Echinodermata 27 206 24 138
Platyhelminthes 3 0 0 0
Nematoda 2 0 0 0
Nemertea 1 0 0 0
Brachiopoda 0 0 0 2
Cnidaria 0 0 0 1
Hemichordata 0 0 0 0
Phoronida 0 0 0 0
Sipuncula 0 0 0 0

3. Species estimation curves

4. Principal Component Analysis

Design 1

Variables have been scaled by mean and standard-deviation prior to analysis.

Design 2

Variables have been scaled by mean and standard-deviation prior to analysis.

Metals at BSI

Variables have been scaled by mean and standard-deviation prior to analysis.

5. Non-metric Multidimensional Scaling

Design 1

Variables have been scaled by mean and standard-deviation prior to analysis.

Design 2

Variables have been scaled by mean and standard-deviation prior to analysis.

Metals at BSI

Variables have been scaled by mean and standard-deviation prior to analysis.

Species

Stations with no species are deleted from this analysis.

6. Hierarchical Agglomerative Clustering

Design 1

Variables have been scaled by mean and standard-deviation prior to analysis.

##  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61 
##   1   2   2   2   2   2   2   2   2   2   3   3   1   3   1   1   3   2 
##  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
##   2   2   2   2   2   2   2   2   2   1   1   1   1   1   1   2   2   2 
##  80  82  83  86  87  88  90  92  93  94  95  96  97  98  99 100 101 102 
##   3   3   3   2   2   2   3   1   1   1   1   3   1   3   1   1   3   2 
## 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 
##   3   3   1   2   1   3   2   2   3   2   2   1   1   3   3   3   1   2 
## 121 122 123 124 125 126 
##   1   1   3   3   1   1

Design 2

Variables have been scaled by mean and standard-deviation prior to analysis.

## 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 
##   1   2   1   1   2   2   2   1   2   2   3   2   2   3   2   3   3   3 
## 119 120 121 122 123 124 125 126 
##   3   2   2   2   3   3   3   2

Metals at BSI

Variables have been scaled by mean and standard-deviation prior to analysis.

## 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 
##   1   2   1   1   3   3   3   1   3   3   3   3   3   3   3   3   2   2 
## 119 120 121 122 123 124 125 126 
##   3   3   3   3   3   2   3   3

Species

Stations with no species are deleted from this analysis.

##  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59  60  61 
##   1   1   1   1   1   1   1   1   1   2   1   1   3   1   2   2   1   2 
##  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79 
##   2   2   1   1   1   1   3   1   2   2   1   1   2   2   1   1   2   2 
##  82  83  86  87  90  92  93  94  95  96  97  98  99 100 101 102 103 104 
##   1   3   1   2   1   2   3   3   1   1   3   1   3   3   1   1   1   1 
## 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 
##   1   1   1   1   1   1   1   3   1   3   1   1   1   1   1   2   1   3 
## 123 124 125 126 
##   1   1   1   1


To assess Section 2, click here.
To go back to Chapter 1’s index page, click here.

Elliot Dreujou

2019-06-12